LAMMPS (10 Mar 2021)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
  1 by 1 by 4 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  create_atoms CPU = 0.002 seconds

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

molecule        dimer molecule.dimer
Read molecule template dimer:
  1 molecules
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9

group		addatoms empty
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute	add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms rigid/nve/small molecule mol dimer
  create bodies CPU = 0.000 seconds
  0 rigid bodies with 0 atoms
  1.0000000 = max distance from body owner to body atom
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 rigid 1
fix		5 addatoms wall/reflect zhi EDGE

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352    1.0079368   -6.8946578   -6.8874992  -0.73775337 
     200      354    1.0081552   -6.8645575    -6.850318  -0.69629729 
     300      356    1.0085803    -6.821677   -6.8004288  -0.69532657 
     400      358    1.0099188   -6.7837923   -6.7555822  -0.68879568 
     500      360    1.0140221   -6.7446709   -6.7094618  -0.72991641 
     600      362     1.026146   -6.7129201   -6.6704003  -0.67063836 
     700      364    1.0683193   -6.6776523   -6.6262908  -0.65572472 
     800      366    1.0958894   -6.6402029   -6.5803182  -0.66307282 
     900      368    1.1231769   -6.6050912   -6.5364187  -0.64076928 
    1000      370    1.1976289   -6.5942508     -6.51333  -0.69249047 
    1100      372      1.05061   -6.5772306   -6.4995645   -0.6307289 
    1200      374   0.93723829   -6.5732962   -6.4981166  -0.64963821 
    1300      376   0.93899122   -6.5578418    -6.476679  -0.65096688 
    1400      378   0.87050694    -6.546852   -6.4662495  -0.67613401 
    1500      380   0.84462904   -6.5400883   -6.4567368  -0.64376986 
    1600      382   0.92417795   -6.5611292   -6.4643567  -0.62092779 
    1700      384   0.67296541   -6.5589985   -6.4845167   -0.6779111 
    1800      386   0.87159158   -6.5655058   -6.4638954   -0.6582786 
    1900      388   0.67504975   -6.5772537   -6.4946123    -0.665098 
    2000      390   0.65034978   -6.5717854   -6.4884072  -0.73162072 
    2100      392   0.63389859   -6.5652907   -6.4803935  -0.64937411 
    2200      394    0.6265637   -6.5582412   -6.4707767  -0.70819854 
    2300      396   0.85352983   -6.5750751   -6.4511408  -0.69995918 
    2400      398   0.69792348   -6.5938659   -6.4886513  -0.63755214 
    2500      400   0.45320495    -6.595022   -6.5242087  -0.70462183 
    2600      402   0.46824374   -6.5697613   -6.4940502  -0.75497893 
    2700      404   0.46605975   -6.5599272   -6.4820583  -0.66778506 
    2800      406   0.50637604   -6.5700492    -6.482743  -0.63812082 
    2900      408   0.55335921   -6.5873352   -6.4890054  -0.62891652 
    3000      410   0.51731142   -6.5890566   -6.4944264  -0.64305355 
    3100      412   0.59439734   -6.6003127   -6.4885025  -0.67140541 
    3200      414   0.53413632    -6.595564   -6.4923492  -0.76242248 
    3300      416   0.49221593   -6.5990831   -6.5014681  -0.71330819 
    3400      418   0.55006126   -6.6015725   -6.4897179  -0.72044309 
    3500      420   0.49065348   -6.6329864   -6.5307669  -0.65775397 
    3600      422   0.41907335   -6.6219753   -6.5325995  -0.75936391 
    3700      424   0.38720116   -6.6153349   -6.5308629  -0.74166397 
    3800      426   0.40625994   -6.6150209   -6.5244231   -0.7595111 
    3900      428   0.40460547   -6.6122642   -6.5200936  -0.70484465 
    4000      430   0.45014991   -6.6254404   -6.5207544  -0.70069933 
    4100      432   0.44820466    -6.640222   -6.5338771    -0.805972 
    4200      434   0.39767521   -6.6450316   -6.5488199  -0.72841414 
    4300      436    0.4155331   -6.6547917   -6.5523381   -0.6894484 
    4400      438   0.43034353   -6.6615074   -6.5534303  -0.74026062 
    4500      440   0.38062977   -6.6541618   -6.5568417  -0.85911194 
    4600      442   0.39357419   -6.6522517   -6.5498512  -0.66232114 
    4700      444   0.40296801   -6.6647029   -6.5580616  -0.67307577 
    4800      446   0.38194993   -6.6510248    -6.548258  -0.77887746 
    4900      448   0.40739835   -6.6601751   -6.5487771  -0.84146416 
    5000      450   0.38392807   -6.6560665   -6.5494198  -0.77343399 
    5100      452   0.35209286   -6.6481476   -6.5488294  -0.68065755 
    5200      454   0.41355143   -6.6615988    -6.543181  -0.81611092 
    5300      456   0.42200484   -6.6627494   -6.5401273   -0.7774134 
    5400      458   0.37764326    -6.661431    -6.550117  -0.72187808 
    5500      460   0.41857405   -6.6674232    -6.542306  -0.74929745 
    5600      462   0.41682611   -6.6710961   -6.5447852   -0.7557454 
    5700      464   0.44396148   -6.6924346   -6.5560887  -0.78018312 
    5800      466   0.37058077   -6.6865013   -6.5711919  -0.74146125 
    5900      468     0.346812    -6.681215     -6.57191  -0.81184233 
    6000      470   0.34919462   -6.6827931    -6.571348  -0.87330821 
    6100      472   0.39360936   -6.6933359   -6.5661634  -0.79237598 
    6200      474   0.33270778   -6.6847095   -6.5759127  -0.77978526 
    6300      476   0.35973804   -6.6951254   -6.5760944  -0.80340174 
    6400      478   0.38124318   -6.7045984   -6.5769857  -0.81628407 
    6500      480   0.41188302   -6.7133356    -6.573896   -0.7940289 
    6600      482   0.36998039   -6.7079555   -6.5813025  -0.75055442 
    6700      484   0.37615026    -6.722917    -6.592741  -0.76534055 
    6800      486    0.3466597   -6.7188712   -6.5976116  -0.77986211 
    6900      488   0.32902492   -6.7247054   -6.6084005  -0.75702458 
    7000      490   0.31856427   -6.7167709   -6.6029979  -0.76014555 
    7100      492   0.30233891   -6.7144406   -6.6053651  -0.96246708 
    7200      494   0.32557309   -6.7315347   -6.6129049   -0.8122153 
    7300      496   0.29919611   -6.7186327   -6.6085455  -0.71917931 
    7400      498   0.29778169   -6.7259455   -6.6153238  -0.88199391 
    7500      500   0.35535305   -6.7419073   -6.6086499  -0.90344083 
    7600      502   0.31979187   -6.7326802   -6.6116434  -0.78324572 
    7700      504   0.30821359     -6.72895   -6.6112295  -0.81363335 
    7800      506   0.31374993   -6.7255461   -6.6046346  -0.89904197 
    7900      508   0.29072338   -6.7177355   -6.6047082  -0.81423073 
    8000      510   0.30557494   -6.7208283    -6.600995  -0.85853575 
    8100      512   0.30521237    -6.726874   -6.6061601  -0.75361257 
    8200      514   0.29622226   -6.7152225   -6.5970794  -0.85766132 
    8300      516   0.28337698   -6.7023552   -6.5884003   -0.8985415 
    8400      518   0.32860902   -6.7211074   -6.5878875  -0.89758921 
    8500      520   0.35483743   -6.7406183   -6.5956126  -0.77602077 
    8600      522   0.32928486   -6.7326607   -6.5970358  -0.75070137 
    8700      524   0.36008106   -6.7474714   -6.5980103  -0.87093836 
    8800      526   0.36082301    -6.743579   -6.5926644  -0.90132107 
    8900      528   0.35010285   -6.7501553   -6.6026214  -0.85238959 
    9000      530   0.31513985   -6.7411795   -6.6073937  -0.75884529 
    9100      532   0.30895083   -6.7421063   -6.6099891  -0.74482692 
    9200      534   0.33631849    -6.751265   -6.6064087  -0.95632911 
    9300      536   0.33306096    -6.759187   -6.6147156  -0.76275935 
    9400      538   0.34582537   -6.7706766    -6.619619  -0.72251598 
    9500      540   0.32003146    -6.772057   -6.6313024  -0.88195851 
    9600      542   0.32439637   -6.7743569   -6.6307127  -0.90233104 
    9700      544   0.33988235   -6.7763721    -6.624862  -0.85185581 
    9800      546   0.32877587   -6.7744977     -6.62697   -0.8550905 
    9900      548   0.29570051   -6.7623752   -6.6288243   -1.0371157 
   10000      550   0.33675914   -6.7757315   -6.6226591   -1.0082157 
Loop time of 16.2553 on 4 procs for 10000 steps with 550 atoms

Performance: 265759.101 tau/day, 615.183 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0034051  | 2.6646     | 8.0317     | 200.7 | 16.39
Bond    | 0.0022626  | 0.0072971  | 0.019437   |   8.3 |  0.04
Neigh   | 0.018657   | 1.218      | 3.7621     | 137.5 |  7.49
Comm    | 1.1497     | 6.7957     | 12.192     | 164.2 | 41.81
Output  | 0.010692   | 0.01431    | 0.019901   |   3.2 |  0.09
Modify  | 3.1502     | 5.3779     | 11.342     | 149.0 | 33.08
Other   |            | 0.1775     |            |       |  1.09

Nlocal:        137.500 ave         299 max           2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost:        1903.75 ave        2686 max         529 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs:        9209.75 ave       23206 max           0 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 36839
Ave neighs/atom = 66.980000
Ave special neighs/atom = 0.36363636
Neighbor list builds = 829
Dangerous builds = 0
Total wall time: 0:00:16
